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Links tagged with 'catalytic domain'

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Found 13 links

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E1DSTool Content

http://e1ds.ee.ncku.edu.tw/

Protein > Interactions, Pathways, Enzymes
Protein > Sequence Features

E1DS is a web server for enzyme catalytic site prediction. Annotation of enzymes is made using a novel pattern mining algorithm that discovers long sequence motifs.

NAR Web Server Issue 2008
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tagsamino acid sequence catalytic domain conserved sequence enzymes protein sequence analysis

firestarTool Content

http://firedb.bioinfo.cnio.es/Php/FireStar.php

Protein > 3-D Structure Comparison
Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes
Sequence Comparison > Multiple Sequence Alignments
Sequence Comparison > Similarity Searching

Firestar predicts functionally important residues, such as catalytic and ligand binding sites, using structural templates and alignment reliability. Prediction coverage has increased with the extension of the FireDB and ligands are now classified for biological relevance.

NAR Web Server Issue 2007NAR Web Server Issue 2011
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tagsalgorithms amino acid sequence amino acid sequence homology amino acids binding sites catalytic domain computational biology ligands molecular models molecular sequence data protein conformation protein databases protein sequence analysis proteins sequence alignment tacrolimus binding proteins

IBISDatabase Content

http://www.ncbi.nlm.nih.gov/Structure/ibis/ibis.cgi

Protein > Databases

IBIS is the NCBI Inferred Biomolecular Interaction Server. This server organizes, analyzes and predicts interaction partners and locations of binding sites in proteins. IBIS provides annotations for different types of binding partners (protein, chemical, nucleic acid and peptides), and facilitates the mapping of a comprehensive biomolecular interaction network for a given protein query.

NAR Database Issue 2010
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tagsalgorithms animals binding sites catalytic domain cluster analysis computational biology genetic databases humans protein databases protein interaction mapping protein-tyrosine kinases tertiary protein structure

INTREPIDTool Content

http://phylogenomics.berkeley.edu/intrepid

Protein > Annotation and Function
Protein > Sequence Features

The INTREPID web server predicts functionally important residues in proteins such as catalytic residues. Users input protein sequence. Residues predicted to be functionally important are displayed on homologous 3D structures if available.

NAR Web Server Issue 2009
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tagsamino acid sequence homology amino acids catalytic domain molecular models phylogeny protein conformation protein sequence analysis proteins

KinasePhos 2.0Tool Content

http://kinasephos2.mbc.nctu.edu.tw/

Protein > Domains and Motifs

KinasePhos 2.0 is a new version of a kinase-specific phosphorylation site prediction tool.

NAR Web Server Issue 2007
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tagscatalytic domain computational biology computer simulation markov chains neural networks (computer) phosphoproteins phosphorylation probability protein kinases protein sequence analysis sensitivity and specificity

PDBSiteScanTool Content

http://wwwmgs.bionet.nsc.ru/mgs/systems/fastprot/pdbsitescan.html

Protein > 3-D Structural Features

PDBSiteScan takes a PDB file as input, and searches for stuctural matches with the PDBSite set of known functional sites.

NAR Web Server Issue 2004
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tagsbinding sites catalytic domain hydrolases intracellular signaling peptides and proteins molecular models oncogene proteins post-translational protein processing proteins tertiary protein structure

PredikinTool Content

http://predikin.biosci.uq.edu.au

Protein > Domains and Motifs
Protein > Interactions, Pathways, Enzymes

The Predikin web server allows users to predict substrates of protein kinases. Users input a protein kinase for evaluation

NAR Web Server Issue 2008
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tagsamino acid sequence animals binding sites catalytic domain mice peptides phosphorylation protein databases protein kinases protein sequence analysis protein-serine-threonine kinases substrate specificity

Protein Geometry DatabaseDatabase Content

http://pgd.science.oregonstate.edu/

Protein > Databases

The Protein Geometry Database (PGD) enables biologists to easily and flexibly query information about the conformation alone, the backbone geometry alone, and the relationships between them. The PGD is valuable for assessing the uniqueness of observed conformational or geometric features in protein structure as well as discovering novel features and principles of protein structure.

NAR Database Issue 2010
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tagsalgorithms amino acid motifs animals catalytic domain computational biology genetic databases humans nucleic acid databases peptides protein databases proteins tertiary protein structure

SAHGDatabase Content

http://bird.cbrc.jp/sahg

Human Genome > Databases
Protein > Databases

The Structure Atlas of Human Genome (SAHG) database contains protein structures encoded in the human genome. All open reading frames in the human genome have been subjected to protein structure prediction.

NAR Database Issue 2011
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tagscatalytic domain humans ligands molecular models protein databases protein interaction mapping protein sequence analysis proteins sequence alignment tertiary protein structure

SBSPKSTool Content

http://www.nii.ac.in/sbspks.html

Protein > 3-D Structural Features
Protein > 3-D Structure Prediction
Protein > Interactions, Pathways, Enzymes

SBSPKS contains web tools for structure based sequence analysis of polyketide synthases. Model_3D_PKS for modeling, visualization and analysis of 3D PKS catalytic domains; Dock_Dom_Anal for identification of key interacting residues in docking, and NRPS-PKS for identification of catalytic domains.

NAR Web Server Issue 2010
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tagscatalytic domain molecular models polyketide synthases protein sequence analysis substrate specificity

SLITHERTool Content

http://bioinfo.mc.ntu.edu.tw/slither/

Protein > 3-D Structural Features
Protein > Biochemical Features
Protein > Molecular Dynamics and Docking

SLITHER is a web server for protein channel studies. It generates contiguous conformations of a molecule along a curved tunnel inside a protein and calculates the ensuing binding free energy profile.

NAR Web Server Issue 2009
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tagscatalytic domain glucose transporter type 1 humans ligands membrane transport proteins molecular models protein conformation

SplitPocketTool Content

http://pocket.uchicago.edu/

Protein > 3-D Structural Features
Protein > Molecular Dynamics and Docking

SplitPocket is a web server for identification of functional surfaces of proteins from their structure coordinates. Identification is based on the geometric concept of a split pocket, which is a pocket split by a binding ligand. >26,000 structures in PDB have been found to have split pockets.

NAR Web Server Issue 2009
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tagscatalytic domain humans ligands mitogen-activated protein kinases molecular models protein conformation proteins src-family kinases

ThYmeDatabase Content

http://www.enzyme.cbirc.iastate.edu

Protein > Databases

The ThYme (Thioester-active enzYme) database has amino acid sequences and 3D (tertiary) structures of all the enzymes constituting the fatty acid synthesis and polyketide synthesis cycles.

NAR Database Issue 2011
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tagsacyltransferases amino acid sequence carbon-carbon ligases catalytic domain fatty acids hydro-lyases ligases macrolides oxidoreductases protein databases tertiary protein structure thiolester hydrolases